German, I thank you very much for you answer. However, I am still confused. I made a small topology file containg only Na+ and Cl- to make sure I understood the parameters before I started working with the large topology file I have for my protein. I used rdparm to pull the LJ parameters out of the topology file and here is what I got:
RDPARM MENU: printLennardJones
Lennard-Jones
Types A C
IP IP 20481.52 15.06
IP IM 739119.15 221.82
IM IM 21121433.30 2906.64
I am having trouble understanding how those numbers are calculated from the sigma and epsilon values given in the parm94 file. Am I missing something? Are the units different or something like that?
Thank you,
Linda Prengaman
Carnegie Mellon University
Dpt. of Chemistry
Class of 2006
>
> Yes, it is possible to do these kind of modifications over the topology
> file but take in mind that Vij = Aij/rij^12-Bij/rij^6...You could put
> different pair-pair interactions....
>
> Good Luck G.
>
>
> At 02:15 p.m. 02/07/2005, you wrote:
>
>> Dear Fellow Amber Users,
>>
>> I have an AMBER6 format topology file for a lignand-protein complex,
>> but I would like to modify the 6-12 lennard-jones parameters for the
>> ligand before I run molecular dynamics. Is it possible (and reasonable)
>> to do that within the topology file? I read about "parameter file
>> formats" in the AMBER6 manual, but I was confused by the ICO indexing.
>> Thank you in advance for any help you can give me.
>>
>> Sincerely, Linda Prengaman Carnegie Mellon University Dept. of Chemistry
>> Class of 2006
>>
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